seatrac_hackday_2024_code
Setup
filter out rare genes and normalize for CD8 and CD4 samples separately
For each dataset, I removed genes with expression in < 20% of samples and with < 10 CPM across samples
CD4 before-and-after removing rare genes
CD8 before-and-after removing rare genes
Voom normalization
CD4
CD8
Model logCFU vs gene
Just CD4_gran samples, association with logCFU
| variable | fdr<0.05 | fdr<0.1 | fdr<0.2 | fdr<0.3 | fdr<0.4 | fdr<0.5 |
|---|---|---|---|---|---|---|
| (1 | subject) | 744 | 936 | 1245 | 1492 | 1785 | 1992 |
| logCFU | 35 | 85 | 482 | 1658 | 2720 | 3997 |
| total (nonredundant) | 779 | 1015 | 1692 | 2988 | 4167 | 5430 |
Just CD4_gran samples, association with logCFU
| variable | fdr<0.05 | fdr<0.1 | fdr<0.2 | fdr<0.3 | fdr<0.4 | fdr<0.5 |
|---|---|---|---|---|---|---|
| (1 | subject) | 861 | 1202 | 1663 | 2106 | 2459 | 2850 |
| logCFU | 25 | 47 | 127 | 219 | 312 | 489 |
| total (nonredundant) | 886 | 1245 | 1780 | 2300 | 2730 | 3254 |
get top hits for low CFU-associated genes in CD4 and CD8
Just CD4_gran samples, genes with negative association with logCFU
$BFSP2
$LOC106998813
$LOC107001007
$LOC697141
$LOC698130
$LOC700872
$LOC702620
$LOC703283
$LOC706087
$LOC708140
$LOC709459
$LOC710859
$LOC712614
$LOC719289
$PSMD9
$SMIM12
$STOX1
Just CD8_gran samples, genes with negative association with logCFU
$ARHGAP19
$BTBD19
$C1H1orf198
$C7H14orf79
$C7H15orf62
$C9H10orf128
$C9H10orf90
$CFAP73
$ENKD1
$ENO3
$HEATR1
$KBTBD8
$LOC100429401
$LOC106997346
$LOC106998746
$LOC707027
$LOC720294
$PDCD1LG2
$RAD54L
$SFXN5
$SLC7A1
$STX3
look for agreement with Bromley
Sig negative corr in any cluster of Bromley, CD4_gran cells in Foreman (FDR < 0.2)
P-values represent interaction between group and logCFU on gene expression
$STOX1
Sig negative corr in any cluster of Bromley, CD8_gran cells in Foreman (FDR < 0.2)
P-values represent interaction between group and logCFU on gene expression
$STX3
$PDCD1LG2
$SLC7A1
$BTBD19
$HEATR1
$ENKD1
$C9H10orf128
$C1H1orf198
$SFXN5
$RAD54L
$ENO3
$C7H15orf62
$C7H14orf79
$ARHGAP19
$CFAP73